When Mark Thompson, a former director general at the BBC, was appointed president and CEO of the New York Times Company, the reaction inside the company was a mix of relief and apprehension. On the one hand, the chairman and publisher, Arthur ­Sulzberger Jr., had finally found a business leader for the long-rudderless Times. On the other, his new hire was fighting allegations that he had been negligent in handling a scandal involving a ­pedophile at the British network. But when Thompson arrived at the Times last fall, uneasiness over Thompson’s problems overseas was soon overwhelmed by anxieties closer to home. Thompson began to appear frequently in the newsroom, and he made it clear he felt very comfortable there.

The Times’ reporters and editors, eager to hold on to the protocols of a legacy media world, hold quasi-religious views about the sanctity of the newsroom against the influence of business concerns. The mere presence of a corporate suit among the journalists was like a belch in a cathedral nave. And yet that view now seems quaint. Sulzberger hired Thompson to transform the Times from a rapidly declining print business into a global, multimedia news brand like the BBC. In August, after the Graham family announced the sale of the Washington Post to Amazon chief Jeff Bezos, Sulzberger and his cousin Michael Golden sent a fevered memo assuring the staff that the ­Sulzbergers were not about to follow suit. Thompson was the family’s firewall against such a fate.

So when the Times communications staff objected to a trip Thompson and executive editor Jill Abramson were planning to take to Silicon Valley last December, arguing that it wasn’t the Times way for the business and news leaders to appear in public together, Sulzberger overrode the concern.

On that trip, Abramson and Thompson went to dinner parties, one at the house of Facebook COO and Lean In author Sheryl Sandberg. At another meeting, Abramson was obliged to defend him, despite having assigned an aggressive investigative reporter to cover his travails at the BBC. During a moderated event at the Commonwealth Club of California, when Abramson was asked by the host where she envisioned the paper five to ten years from now, she laughed sardonically and peered into the audience. “Mark, would you like to handle this question?” she asked. “No, I’m just kidding.”

But the joke contained an uneasy truth: The role of “visionary” at the paper, traditionally held by the news chief, was now being ceded to Thompson. And in recent months, say several Times sources, Abramson has chafed at some of Thompson’s moves as he redirects company resources to projects of ambiguous design, including an aggressive video unit run by a former AOL/Huffington Post executive who sits among news editors but reports to the corporate side of the Times.

Thompson and I met in his office on the sixteenth floor of the Times building to talk about his plans. He is the first leader to come from outside the Times hierarchy. He spoke about building out a smorgasbord of “news products” to sell to more potential subscribers, including online puzzles and games and a Times-sponsored cruise with editors and reporters to Europe. He discussed a multimedia magazine, a project involving food and dining, and conferences starring Times columnists and hosted by paid advertisers—like the one that featured business writer Andrew Ross Sorkin interviewing the CEO of Goldman Sachs last December and was sponsored by Research in Motion.

What he described is a company where the news itself was a starting point for a brand—not a novel position among media companies now, but one he plans to pursue vigorously in a newspaper culture that’s never much appreciated vigorous change. “The problem many American publications have got is a loss of creative focus,” he told me. “The business-model issues, in the end, are kind of second order.”

When Arthur Sulzberger first met with Mark Thompson in London last spring, he was under duress. Advertising was plummeting, and revenue from the pay wall, the much-heralded plan to charge readers for access to the website, had begun to plateau. Sulzberger had fired the former CEO, Janet Robinson, a longtime Times advertising executive, in December 2011, leaving the company without a business leader for a long period in a dangerous era.

Thompson was hailed by Sulzberger as something the Times didn’t seem to have in house: a digital visionary. Its own ­version of a web guru, Martin Nisenholtz, had been marginalized by Robinson after a protracted battle over whether the pay wall was a good idea (she was for it; he was against). Robinson was fired, in part because she came up against Michael Golden. As part of her exit, the Times had to shell out roughly $24 million in compensation.